I've adjusted your question to be more research, fact and reference oriented; to avoid it being closed for being not constructive. +1 Your question is very interesting, although I think we should look at "being organized causes productivity" in general as it will be hard to find such specific research. I wonder whether we just took this as a fact or if there really has been done research to point this out...
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Tom WijsmanJun 25 '11 at 9:36

2

Yes, but I can't find it under the mess on my desk ;-)
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Brian CarltonJun 25 '11 at 18:05

Great question. I am a "messy desk person" and keep hearing about clearing it to be more productive. But I find my mess helpful at times. I think I might dig for that research we are after here...
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Dmitry SelitskiyJun 28 '11 at 1:07

I've always been an adept to the idea that cleaning up my desk = clearing up my mind before starting work.
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Mihai OpreaJul 1 '11 at 11:36

4 Answers
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There's a difference between mess and disorganization. I can have a dozen piles of paper on my desk - each for one task. I know exactly where everything is. Although it appears messy to others, it is organized and aids in task switching/productivity. Then there is disorganization where everything is one giant pile or things get lost. Disorganization does harm productivity because one wastes time looking for things.

I think to measure correlation between messiness and productivity, the personality of the individual needs to be taken into account.

As an embedded engineer, my desk is always in a constant state of mess. Check out these desks. Engineer's messy desk The late owners of these desks are extremely productivity in their domains, but their desk are truly a mess!

Proper answer

The link Robby Slaughter posted has it right. Every single thing you have on a desk will demand your attention by default. That's the reaction that someone else gets when they first see it.

Eventually, your brain will learn to filter out some of that mess and start organizing it mentally. Like it will know that this pile of junk is where you keep tools. That pile is where you keep your forms dedicated to doing a specific task.

However, this doesn't necessarily make it more organized. When you drop something in the wrong pile, it will be nearly impossible to find. It also means that everything that isn't in the stacks of useful things will be filtered out by your brain and ignored, meaning that you can have actual garbage lying somewhere between the stacks and never see it.

I would recommend cleaning up your desk if you plan to have other people work with it and so you don't have candy wrappers and moldy sandwiches hidden in there somewhere. An organized mess can easily be an organized non-mess, and it takes little effort to maintain it in some cases.

Realistic answer

The time spent cleaning it up is not always worth the productivity gain from a clean desk.

And as most people know, a clean area attracts mess. If your desk is clean and your colleague's is cluttered, your boss may choose to dump their excess things on your desk because there's more space.

People will also correlate messy desks with work, so if your desk is clean, you may be given more work (since you've obviously got a lot of time to clean your things). Or if they see that your "to do" stack is small and neat, they may think that you've got room for more work.

If you are in full control, clean it up. Otherwise, organized chaos may be your best option.